2V6K

Structure of Maleyl Pyruvate Isomerase, a bacterial glutathione-s- transferase in Zeta class, in complex with substrate analogue dicarboxyethyl glutathione

PDB DOI: 10.2210/pdb2V6K/pdb

Classification: ISOMERASE
Organism(s): Ralstonia sp. U2
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2007-07-19 Released: 2008-07-22
Deposition Author(s): Shoemark, D.K., Zhou, N.-Y., Williams, P.A., Hadfield, A.T.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.30 Å
R-Value Free: 0.165
R-Value Work: 0.150
R-Value Observed: 0.151

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

Structure of Bacterial Glutathione-S-Transferase Maleyl Pyruvate Isomerase and Implications for Mechanism of Isomerisation.

Marsh, M., Shoemark, D.K., Jacob, A., Robinson, C., Cahill, B., Zhou, N.-Y., Williams, P.A., Hadfield, A.T.

(2008) J Mol Biol 384: 165

PubMed: 18824004 Search on PubMed
DOI: 10.1016/j.jmb.2008.09.028
Primary Citation of Related Structures:
2JL4, 2V6K

PubMed Abstract:

Maleyl pyruvate isomerase (MPI) is a bacterial glutathione S-transferase (GST) from the pathway for degradation of naphthalene via gentisate that enables the bacterium Ralstonia to use polyaromatic hydrocarbons as a sole carbon source. Genome sequencing projects have revealed the presence of large numbers of GSTs in bacterial genomes, often located within gene clusters encoding the degradation of different aromatic compounds. This structure is therefore an example of this under-represented class of enzymes. Unlike many glutathione transferases, the reaction catalysed by MPI is an isomerisation of an aromatic ring breakdown product, and glutathione is a true cofactor rather than a substrate in the reaction. We have solved the structure of the enzyme in complex with dicarboxyethyl glutathione, an analogue of a proposed reaction intermediate, at a resolution of 1.3 A. The structure provides direct evidence that the glutathione thiolate attacks the substrate in the C2 position, with the terminal carboxylate buried at the base of the active site cleft. Our structures suggest that the C1-C2 bond remains fixed so when rotation occurs around the C2-C3 bond the atoms from C4 onwards actually move. We identified a conserved arginine that is likely to stabilize the enolate form of the substrate during the isomerisation. Arginines at either side of the active site cleft can interact with the end of the substrate/product and preferentially stabilise the product. MPI has significant sequence similarity to maleylacetoacetate isomerase (MAAI), which performs an analogous reaction in the catabolism of phenylalanine and tyrosine. The proposed mechanism therefore has relevance to the MAAIs. Significantly, whilst the overall sequence identity is 40% only one of the five residues from the Zeta motif in the active site is conserved. We re-examined the roles of the residues in the active site of both enzymes and the Zeta motif itself.

Related Citations:

A Gene Cluster Encoding Steps in Conversion of Naphthalene to Gentisate in Pseudomonas Sp. Strain U2
Fuenmayor, S.L., Wild, M., Williams, P.A.
(1998) J Bacteriol 9: 2522

Organizational Affiliation:

Department of Biochemistry and Centre for Molecular Recognition, University of Bristol, School of Medical Sciences, University Walk, Bristol BS81TD, UK.

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
MALEYLPYRUVATE ISOMERASE	A, B	214	Ralstonia sp. U2	Mutation(s): 0 EC: 5.2.1.2 (PDB Primary Data), 5.2.1.4 (UniProt)
UniProt
Find proteins for O86043 (Ralstonia sp) Explore O86043 Go to UniProtKB: O86043
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O86043
Protein Feature View Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
TGG Query on TGG Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain F [auth B] MOL2 format, chain C [auth A] MOL2 format, chain F [auth B]	C [auth A], F [auth B]	GAMMA-GLUTAMYL-S-(1,2-DICARBOXYETHYL)CYSTEINYLGLYCINE C₁₄ H₂₁ N₃ O₁₀ S PWCIUOASSAHGHI-BIIVOSGPSA-N		Ligand Interaction
ACT Query on ACT Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain H [auth B] MOL2 format, chain E [auth A] MOL2 format, chain H [auth B]	E [auth A], H [auth B]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Ligand Interaction
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain G [auth B] MOL2 format, chain D [auth A] MOL2 format, chain G [auth B]	D [auth A], G [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Ligand Interaction